Phenotype plots

Source Code

rm(list = ls())
source('~/YeastProj.dir/evogen-sims/ET_Yeast/Writing1.dir/Code.dir/PhenotypePlotCode.R')

Neutral selection

dirpath <- "~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/NS.dir/"
pattern <- "^MeanPhenotypes(1|2|3)_n\\d+_H0.1_*" #|10|15|20|30
# "^MeanPhenotypes15\\D" #(\\D|$).    (1|2|3|10|13|17|21)_n
result <- process_files(dirpath, pattern, "loci")
plots <- result$plots
plots

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NS, CS, and SinFS single locus

pheno1 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/NS.dir/MeanPhenotypes1_n1_H0.8.csv")
p1 <- pheno1 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

pheno2 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/CS.dir/MeanPhenotypes1_n1_H0.8SD2.csv")
p2 <- pheno2 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

pheno3 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/SinFSGen.dir/MeanPhenotypes1_n1_H0.8SD2.csv")
p3 <- pheno3 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

p1/p2/p3

Constant selection

dirpath <- "~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/CS.dir/"
pattern <- "^MeanPhenotypes(1|2|3)_n*" #|10|15|20|30
# "^MeanPhenotypes15\\D" #(\\D|$).    (1|2|3|10|13|17|21)_n
result <- process_files(dirpath, pattern, "loci")
#combined_data <- result$combined_data
#plots <- result$plots
result$plots

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Fluctuating Linear

dirpath <- "~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/LinFS.dir/"
pattern <- "^MeanPhenotypes(1|2|3|10|15|20|30)_n*"
result <- process_files(dirpath, pattern, "loci_gen")
#combined_data <- result$combined_data
#plots <- result$plots

result$plots

$`loci = 1 gen = 10`

$`loci = 1 gen = 20`

$`loci = 1 gen = 30`

$`loci = 10 gen = 10`

$`loci = 10 gen = 20`

$`loci = 10 gen = 30`

$`loci = 100 gen = 10`

$`loci = 100 gen = 20`

$`loci = 100 gen = 30`

$`loci = 300 gen = 10`

$`loci = 300 gen = 20`

$`loci = 300 gen = 30`

$`loci = 70 gen = 10`

$`loci = 70 gen = 20`

$`loci = 70 gen = 30`

pheno1 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/LinFS.dir/MeanPhenotypes10_n1_H0.1SD1Gen10.csv")
p1 <- pheno1 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

pheno2 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/LinFS.dir/MeanPhenotypes10_n1_H0.5SD1Gen10.csv")
p2 <- pheno2 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

pheno3 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/LinFS.dir/MeanPhenotypes10_n1_H0.8SD1Gen10.csv")
p3 <- pheno3 %>% ggplot(aes(Generation, Phenotype))+
  geom_line()

p1/p2/p3

geno1 <- read.csv("~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/LinFS.dir/genome10_n10_H0.1SD4Gen10.csv")
ggplotly(geno1 %>% ggplot(aes(Generation, Frequency, color = interaction(Position,Effect), group = interaction(Position,Effect), linetypes = interaction(Position,Effect)))+
  geom_line())

Fluctuating Sinusoidal I

dirpath <- "~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/SinFS.dir/"
pattern <- "^MeanPhenotypes(1|2|3|10|15|20|30)_n*"
result <- process_files(dirpath, pattern, "loci_gen")
#combined_data <- result$combined_data
#plots <- result$plots
result$plots

$`loci = 1 gen = 10`

$`loci = 1 gen = 20`

$`loci = 1 gen = 30`

$`loci = 10 gen = 10`

$`loci = 10 gen = 20`

$`loci = 10 gen = 30`

$`loci = 100 gen = 10`

$`loci = 100 gen = 20`

$`loci = 100 gen = 30`

$`loci = 300 gen = 10`

$`loci = 300 gen = 20`

$`loci = 300 gen = 30`

$`loci = 70 gen = 10`

$`loci = 70 gen = 20`

$`loci = 70 gen = 30`

Fluctuating Sinusoidal II

dirpath <- "~/YeastProj.dir/evogen-sims/ET_Yeast/output.dir/Selection_Models/WF.dir/SinFSGen.dir/" 
pattern <- "^MeanPhenotypes(1|2|3|10|15|20|30)_n*" 
result <- process_files(dirpath, pattern, "loci") 
#combined_data <- result$combined_data 
#plots <- result$plots 
result$plots

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